Pool male and female individuals for de novo transcriptome assembly?

Question

[nsimons]

Hi, I have what I think is a simple question:

Is it appropriate to combine reads from males and females for de novo transcriptome assembly?

I have an RNAseq dataset consisting of 8 females and 21 males, I've done a de novo assembly on a single individual as a first pass and it looks pretty good, but it makes sense to leverage the amount of data I have for a more complete transcriptome. Is there any potential issue with combining both sexes?

Thanks!

Answer 1

[WouterDeCoster]

Well, apart from sex chromosomes and gender-specific expression on those, I don't think there is a reason not to combine all your data.

As a sanity check, you could also assemble all males and compare that to the assembly of all animals.